I will share what I figured out:
It is NOT the plugin that is the problem.
From CCS Website:
MPLAB X IDE Plug-in dated 23-May-16
This shows up under MPLAB x V5.xxx as
Version: 3.13 Source: Micr ...
I installed CCS V5.103 as suggested.
I have MPLAB X V5.50
But the Makefile is still not generated correctly by MPLAB X, even with the CCS V5.103 plugin.